eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows for: (i) de novo gene prediction from raw contigs, (ii) built-in pairwise orthology prediction, (iii) fast protein domain discovery, and (iv) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.

eggNOG-mapper v2: Functional Annotation, Orthology Assignments, and Domain Prediction at the Metagenomic Scale

Even though automated functional annotation of genes represents a fundamental step in most genomic and metagenomic workflows, it remains challenging at large scales. Here, we describe a major upgrade to eggNOG-mapper, a tool for functional annotation based on precomputed orthology assignments, now optimized for vast (meta)genomic data sets. Improvements in version 2 include a full update of both the genomes and functional databases to those from eggNOG v5, as well as several efficiency enhancements and new features. Most notably, eggNOG-mapper v2 now allows: (i) de novo gene prediction from raw contigs, (ii) built-in pairwise orthology prediction, (iii) fast protein domain discovery, and (iv) automated GFF decoration. eggNOG-mapper v2 is available as a standalone tool or as an online service at http://eggnog-mapper.embl.de.

Cable Angle and Minimum Resultant Force Response Analysis of Lower Limb Traction Device for Rehabilitation Robot With Interval Parameters

This paper proposes a hybrid uncertainty analysis method (HUAM) based on the first-order interval perturbation method (FIPM) and Monte Carlo method (MCM) for minimum resultant force response analysis of the lower limb traction device (LLTD) of a hybrid-driven parallel waist rehabilitation robot (HDPWRR) with interval parameters. Based on the analysis of cable angles by using the interval algorithm, the problem of non-uniqueness of the force solution in redundant constraint mechanisms is solved. The force response domain prediction with interval parameters on rehabilitation patients is estimated by using the HUAM which combining the first-order interval perturbation technique with direct Monte Carlo method in different stages, and it reduces the calculation amount. First, the kinematic and static models of the LLTD with deterministic information are established according to its work principle. Then, the interval matrices with interval parameters are calculated by using the FIPM and the response of cable angles is combined with the static model. Third, by numerical examples, the accuracy and efficiency of the HUAM for solving the force response domain problem with interval parameters are verified. The bounds of cable angle response domain of the interval LLTD model are determined. Finally, the minimum resultant force response domain prediction with interval parameters on rehabilitation patients is estimated by combining the FIPM and MCM.